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- PDB-4ify: HIV-1 reverse transcriptase with bound fragment at the Knuckles site -

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Basic information

Entry
Database: PDB / ID: 4ify
TitleHIV-1 reverse transcriptase with bound fragment at the Knuckles site
Components
  • REVERSE TRANSCRIPTASE/RIBONUCLEASE H
  • p51 RT
Keywordstransferase/transferase inhibitor / RNA-DIRECTED DNA POLYMERASE / DNA POLYMERASE / ENDONUCLEASE / HYDROLASE / MULTIFUNCTIONAL ENZYME / transferase-transferase inhibitor complex
Function / homology
Function and homology information


HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / symbiont-mediated suppression of host gene expression / viral penetration into host nucleus / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / viral translational frameshifting / lipid binding / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / DNA binding / zinc ion binding / membrane
Similarity search - Function
HIV Type 1 Reverse Transcriptase, subunit A, domain 1 / HIV Type 1 Reverse Transcriptase; Chain A, domain 1 / Reverse transcriptase/Diguanylate cyclase domain / Ribonuclease H-like superfamily/Ribonuclease H / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. ...HIV Type 1 Reverse Transcriptase, subunit A, domain 1 / HIV Type 1 Reverse Transcriptase; Chain A, domain 1 / Reverse transcriptase/Diguanylate cyclase domain / Ribonuclease H-like superfamily/Ribonuclease H / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retropepsin-like catalytic domain / RNase H type-1 domain profile. / Ribonuclease H domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase (RNA-dependent DNA polymerase) / Retroviral matrix protein / Retrovirus capsid, C-terminal / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Nucleotidyltransferase; domain 5 / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Ribonuclease H superfamily / Aspartic peptidase domain superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / Roll / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
1-[4-(trifluoromethoxy)phenyl]methanamine / Chem-T27 / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBauman, J.D. / Patel, D. / Arnold, E.
CitationJournal: J.Med.Chem. / Year: 2013
Title: Detecting Allosteric Sites of HIV-1 Reverse Transcriptase by X-ray Crystallographic Fragment Screening.
Authors: Bauman, J.D. / Patel, D. / Dharia, C. / Fromer, M.W. / Ahmed, S. / Frenkel, Y. / Vijayan, R.S. / Eck, J.T. / Ho, W.C. / Das, K. / Shatkin, A.J. / Arnold, E.
History
DepositionDec 15, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2013Group: Database references
Revision 1.2Jun 17, 2015Group: Non-polymer description
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: REVERSE TRANSCRIPTASE/RIBONUCLEASE H
B: p51 RT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,91821
Polymers114,0862
Non-polymers1,83219
Water11,926662
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9080 Å2
ΔGint5 kcal/mol
Surface area46040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.946, 73.051, 108.755
Angle α, β, γ (deg.)90.00, 100.47, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein REVERSE TRANSCRIPTASE/RIBONUCLEASE H / EXORIBONUCLEASE H / P66 RT


Mass: 63989.238 Da / Num. of mol.: 1 / Fragment: P66 (unp residues 600-1154) / Mutation: K771A, K772A, C879S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 / Strain: BH10 / Gene: gag-pol, POL / Plasmid: PCDF-2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(RIL)
References: UniProt: P03366, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H
#2: Protein p51 RT / Gag-Pol polyprotein


Mass: 50096.539 Da / Num. of mol.: 1 / Fragment: P51 (unp residues 600-1027) / Mutation: C879S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 / Strain: BH10 / Gene: gag-pol, POL / Plasmid: PCDF-2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(RIL)
References: UniProt: P03366, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H

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Non-polymers , 5 types, 681 molecules

#3: Chemical ChemComp-T27 / 4-{[4-({4-[(E)-2-cyanoethenyl]-2,6-dimethylphenyl}amino)pyrimidin-2-yl]amino}benzonitrile / Rilpivirine


Mass: 366.419 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H18N6 / Comment: medication, inhibitor*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical ChemComp-1FD / 1-[4-(trifluoromethoxy)phenyl]methanamine


Mass: 191.150 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8F3NO
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 662 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.63 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 11% PEG 8000, 4% PEG 400, 50 MM IMIDAZOLE, 10 MM SPERMINE, 15 MM MGSO4, 100 MM AMMONIUM SULFATE, AND 5 MM TRIS(2-CARBOXYETHYL)PHOSPHINE, PH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.917
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 20, 2008
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.917 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 73811 / Num. obs: 73738 / % possible obs: 99.9 % / Observed criterion σ(F): -2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 17.4
Reflection shell
Resolution (Å)Rmerge(I) obsDiffraction-ID% possible all
2.1-2.140.629199.8
2.14-2.180.529199.7
2.18-2.220.505199.8
2.22-2.260.456199.8
2.26-2.310.418199.8
2.31-2.370.352199.9

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Processing

Software
NameVersionClassification
Adxvdata processing
PHENIX(phenix.refine: dev_1233)model building
PHENIX(phenix.refine: dev_1233)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXdev_1233phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→31.312 Å / SU ML: 0.24 / σ(F): 1.35 / Phase error: 22.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2126 1447 1.98 %2%
Rwork0.1864 ---
obs0.1869 72971 99.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→31.312 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7929 0 106 662 8697
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098246
X-RAY DIFFRACTIONf_angle_d1.1911189
X-RAY DIFFRACTIONf_dihedral_angle_d14.693108
X-RAY DIFFRACTIONf_chiral_restr0.0891202
X-RAY DIFFRACTIONf_plane_restr0.0061401
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.1750.28531450.23897076X-RAY DIFFRACTION100
2.175-2.26210.27221510.2337090X-RAY DIFFRACTION100
2.2621-2.3650.26821460.21757121X-RAY DIFFRACTION100
2.365-2.48970.24381460.21357074X-RAY DIFFRACTION100
2.4897-2.64560.25621190.19827170X-RAY DIFFRACTION100
2.6456-2.84970.23821610.19757163X-RAY DIFFRACTION100
2.8497-3.13630.23931500.19447126X-RAY DIFFRACTION100
3.1363-3.58950.21071280.17837185X-RAY DIFFRACTION100
3.5895-4.52020.19491440.15897209X-RAY DIFFRACTION100
4.5202-31.31520.16291570.17617310X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.2091-0.4228-0.9741.1480.35492.79290.052-0.4426-0.26160.2046-0.01870.1820.27620.1916-0.02380.51150.01240.06240.31630.01620.219246.7205-15.425970.0805
20.8174-0.18510.40910.93182.14745.04860.0768-0.1581-0.23560.24330.11240.21550.6769-0.6283-0.16890.48140.02240.01070.360.04570.35639.8396-17.671858.6897
30.5197-0.2064-0.2760.3390.99994.4097-0.0022-0.2051-0.19510.24480.13520.07810.46620.1585-0.13250.35990.03320.03220.25850.02940.236648.1516-18.656961.7097
43.0172-0.11742.03721.04020.32232.79030.4449-0.3364-0.84180.25280.05670.04920.5983-0.0669-0.48690.4317-0.0161-0.08110.20150.06840.375650.9081-28.653742.6935
52.17780.57330.85773.3183-1.63292.8790.0805-0.1784-0.16240.29310.29620.63520.0824-0.6067-0.34830.2388-0.00340.02590.26040.02090.307129.4147-19.454624.8424
63.2963-1.78711.36611.2915-0.7570.5925-0.0469-0.1887-0.0530.08350.11650.15960.0663-0.1201-0.06360.135-0.00660.0380.2209-0.0240.210320.05562.57817.417
74.21251.0092-0.38151.2365-1.12491.1291-0.0122-0.20710.7149-0.4245-0.46331.0488-0.7856-0.91960.30540.34070.1602-0.10890.4743-0.14290.509113.211517.51924.0767
84.8765-1.12640.6724.9060.47264.5391-0.10210.14730.38130.2661-0.0093-0.271-0.53220.44140.04030.2436-0.0876-0.03570.1660.05450.179656.40551.417936.4478
90.60851.8239-1.68987.4007-6.15385.2850.1915-0.40550.94221.685-0.3366-0.0421-2.27541.63140.11960.9397-0.2956-0.2130.70820.10910.815255.914125.979233.4785
101.4291-0.73960.61112.4314-1.36271.3613-0.16310.39960.76560.3524-0.321-0.7643-0.59970.80930.43840.5782-0.3189-0.14880.54480.1910.644764.33513.558831.9501
113.8029-0.8521.43521.9364-0.32231.0204-0.2388-0.257-0.30850.497-0.1254-0.6172-0.10940.60430.34790.3738-0.09940.010.79670.27950.576951.154620.671810.8243
122.01920.48512.62523.1334-0.15935.2056-0.1392-0.08360.40440.2615-0.086-0.0223-0.4011-0.06430.30160.18-0.07670.08950.224-0.01110.202832.229824.94298.6194
133.3877-0.61380.74166.6184-1.03481.83930.150.07320.27950.2548-0.2936-0.0998-0.16180.14550.13710.199-0.04270.02290.1976-0.00290.137643.208210.335120.2119
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 59 )
2X-RAY DIFFRACTION2chain 'A' and (resid 60 through 96 )
3X-RAY DIFFRACTION3chain 'A' and (resid 97 through 155 )
4X-RAY DIFFRACTION4chain 'A' and (resid 156 through 253 )
5X-RAY DIFFRACTION5chain 'A' and (resid 254 through 383 )
6X-RAY DIFFRACTION6chain 'A' and (resid 384 through 527 )
7X-RAY DIFFRACTION7chain 'A' and (resid 528 through 554 )
8X-RAY DIFFRACTION8chain 'B' and (resid 5 through 83 )
9X-RAY DIFFRACTION9chain 'B' and (resid 84 through 104 )
10X-RAY DIFFRACTION10chain 'B' and (resid 105 through 211 )
11X-RAY DIFFRACTION11chain 'B' and (resid 212 through 253 )
12X-RAY DIFFRACTION12chain 'B' and (resid 254 through 363 )
13X-RAY DIFFRACTION13chain 'B' and (resid 364 through 428 )

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